California condor genome data and resources

Genome assembly for the California condor, genotype data for two California condors and two related species (Andean condor and turkey vulture), and supporting files.

See "Genome-wide diversity in the California condor tracks its prehistoric abundance and decline," by Robinson et al. (2021) for full details. Also see https://10.5281/zenodo.4680034 for processing and analysis code.

Samples:
CRW1112 California condor (Studbook #593)
CYW1141 California condor (Studbook #309)
VulGry1 Andean condor (ISIS 417)
BGI_N323 Turkey vulture (SAMN02319050, from https://doi.org/10.1126/science.1251385)

Files:
gc_PacBio_HiC.fasta California condor genome sequence.

gc_PacBio_HiC_scaffold_chr_key.txt Key giving the chromosomal identity of scaffolds in the California condor genome assembly (where known).

gc_PacBio_HiC_repeats*.bed Coordinates of repeats in the California condor genome identified with Tandem Repeats Finder (TRF, https://tandem.bu.edu/trf/trf.html) and WindowMasker (WM, https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker).

*.vcf.gz, *.vcf.gz.tbi Raw VCF files plus indexes for each sample aligned to reference gc_PacBio_HiC.fasta. 

*cpgIslands*.bed Coordinates of CpG islands in gc_PacBio_HiC.fasta. Coordinates including and excluding CpG islands in repeats are provided.

*.over.chain.gz, *.rbest.chain.gz Chain files for liftOver (https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64). Named as FROM.TO.TYPE.chain.gz. The "rbest" chains represent the reciprocal best alignments between both genomes. ASM69994v1 is the turkey vulture genome assembly, galGal6 is the chicken genome assembly.

ismc_CYW1141.rho.*.bed Bed files containing coordinate ranges and rho/bp inferred with iSMC (https://github.com/gvbarroso/iSMC) using California condor #309. Intervals of 1 kb and 1 Mb are provided.

*.psmc, *.msmc, *.msmc2 Output files from PSMC (https://github.com/lh3/psmc), MSMC (https://github.com/stschiff/msmc), and MSMC2 (https://github.com/stschiff/msmc2).

ROH*.bed Coordinates of runs of homozygosity (ROH) >=1 Mb in each California condor sample, identified with Plink (v1.9, https://www.cog-genomics.org/plink/).